My Mini is the same as yours and came with 2 HDD @ 1TB each. There are 2 basic options for adding storage, internal or external. You said you are not using Plex, but if your are using iTunes to manage you files, then your Media folder can be on either drive, but it will be less than 750GB or so on the system drive or up to to 1TB if on the 2nd drive.
What I did was install a internal larger 2TB drive in the 2nd HHD slot and put the media folder there. Not too hard, just follow the ifixit videos. While a bit more trouble than an USB external drive, my iTunes media is all self contained
The external USB3 2.5" drive options until just recently were limited to 2TB. There are now relatively cheap 4TB USB3 2.5" drives and if and when my Media folder gets above 2TB, this is the option I will most likely use. I just bought another 4TB drive this weekend for $119 delivered from B&H. The ones I use are the Seagate Backup Plus, which are actually Samsung drives internally, not Seagate. Been using the 2TB ones for a couple of years without incident.